UPDATE HTML FILE on public

public/_sources/page1.rst.txt

@@ -46,6 +46,66 @@ stable and complete version of Raspbian by using NOOBS (a simple-to-use operatin
 Once the OS has been installed, the 1-wire option and GPIO remote option must be deactivated via the
 Raspbian GUI settings menu. Failure to carry out this task may cause damage to the relay shield cards during measurements.
 
+.. note:: 
+	 All the development tests were performed on Raspberry Pi 3 Model B, we used the following version of Raspbian:
+	 
+	 .. figure:: raspbian_version.jpg
+	   :width: 800px
+	   :align: center
+	   :height: 400px
+	   :alt: alternate text
+	   :figclass: align-center
+
+Virtual Environnement and packages
+***********************************************
+
+All dependencies are specified in requirements.txt
+
+.. note:: 
+	 all instructions below should be typed in the terminal
+
+It is first necessary to ensure that the libatlas-base-dev library is installed:
+
+.. code-block:: python
+	
+	 sudo apt-get install libatlas-base-dev
+
+We strongly recommend users to create a virtual environment to run the code and installed all required dependencies. It can be done either in a directory gathering all virtual environments used on the computer or within the ohmpy directory.
+
+create the virtual environment:
+
+.. code-block:: python
+	 
+	 python3 -m venv ohmpy
+
+activate it using the following command:
+
+.. code-block:: python
+	 
+	 source ohmpy/bin/activate
+
+install packages within the virtual environment. Installing the following package should be sufficient to meet dependencies:
+
+.. code-block:: python
+	 
+	 pip install RPi.GPIO adafruit-blinka numpy adafruit-circuitpython-ads1x15 pandas
+
+check that requirements are met using 
+
+.. code-block:: python
+	 
+	 pip list
+
+you should run you code within the virtual environment
+to leave the virtual environment simply type:
+
+.. code-block:: python
+	  
+	 deactivate
+
+
+Running thonny on Rapberry Pi 
+**************************************************************************
 
 
 

public/index.html

@@ -158,7 +158,7 @@
 <dd class="field-odd"><p>open hardware resistivity-meter</p>
 </dd>
 <dt class="field-even">Date</dt>
-<dd class="field-even"><p>Aug 24, 2020</p>
+<dd class="field-even"><p>Nov 14, 2020</p>
 </dd>
 <dt class="field-odd">Authors</dt>
 <dd class="field-odd"><p><strong>Rémi CLEMENT, Nicolas FORQUET, Julien GANCE, Yannick FARGIER, Vivien DUBOIS, Hélène GUYARD</strong></p>
@@ -191,6 +191,8 @@
 <li class="toctree-l2"><a class="reference internal" href="page1.html#the-philosophy-of-ohmpi">The philosophy of Ohmpi</a></li>
 <li class="toctree-l2"><a class="reference internal" href="page1.html#technical-data">Technical data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="page1.html#os-installation-on-a-raspberry-pi">OS installation on a Raspberry Pi</a></li>
+<li class="toctree-l2"><a class="reference internal" href="page1.html#virtual-environnement-and-packages">Virtual Environnement and packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="page1.html#running-thonny-on-rapberry-pi">Running thonny on Rapberry Pi</a></li>
 <li class="toctree-l2"><a class="reference internal" href="page1.html#construction-of-the-measurement-board-and-connection-to-the-raspberry">Construction of the measurement board and connection to the Raspberry</a></li>
 <li class="toctree-l2"><a class="reference internal" href="page1.html#current-injection">Current injection</a></li>
 <li class="toctree-l2"><a class="reference internal" href="page1.html#multiplexer-implentation">Multiplexer implentation</a></li>

public/page1.html

@@ -87,6 +87,8 @@
 <li class="toctree-l2"><a class="reference internal" href="#the-philosophy-of-ohmpi">The philosophy of Ohmpi</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#technical-data">Technical data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#os-installation-on-a-raspberry-pi">OS installation on a Raspberry Pi</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#virtual-environnement-and-packages">Virtual Environnement and packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#running-thonny-on-rapberry-pi">Running thonny on Rapberry Pi</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#construction-of-the-measurement-board-and-connection-to-the-raspberry">Construction of the measurement board and connection to the Raspberry</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#electrical-resistivity-measurements">Electrical resistivity measurements</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#implementation">Implementation</a></li>
@@ -241,6 +243,50 @@ For this step, the installation instructions are well described on the Raspberry
 stable and complete version of Raspbian by using NOOBS (a simple-to-use operating system installer).
 Once the OS has been installed, the 1-wire option and GPIO remote option must be deactivated via the
 Raspbian GUI settings menu. Failure to carry out this task may cause damage to the relay shield cards during measurements.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>All the development tests were performed on Raspberry Pi 3 Model B, we used the following version of Raspbian:</p>
+<div class="align-center figure">
+<a class="reference internal image-reference" href="_images/raspbian_version.jpg"><img alt="alternate text" src="_images/raspbian_version.jpg" style="width: 800px; height: 400px;" /></a>
+</div>
+</div>
+</div>
+<div class="section" id="virtual-environnement-and-packages">
+<h2>Virtual Environnement and packages<a class="headerlink" href="#virtual-environnement-and-packages" title="Permalink to this headline">¶</a></h2>
+<p>All dependencies are specified in requirements.txt</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>all instructions below should be typed in the terminal</p>
+</div>
+<p>It is first necessary to ensure that the libatlas-base-dev library is installed:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">libatlas</span><span class="o">-</span><span class="n">base</span><span class="o">-</span><span class="n">dev</span>
+</pre></div>
+</div>
+<p>We strongly recommend users to create a virtual environment to run the code and installed all required dependencies. It can be done either in a directory gathering all virtual environments used on the computer or within the ohmpy directory.</p>
+<p>create the virtual environment:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">venv</span> <span class="n">ohmpy</span>
+</pre></div>
+</div>
+<p>activate it using the following command:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">source</span> <span class="n">ohmpy</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">activate</span>
+</pre></div>
+</div>
+<p>install packages within the virtual environment. Installing the following package should be sufficient to meet dependencies:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">RPi</span><span class="o">.</span><span class="n">GPIO</span> <span class="n">adafruit</span><span class="o">-</span><span class="n">blinka</span> <span class="n">numpy</span> <span class="n">adafruit</span><span class="o">-</span><span class="n">circuitpython</span><span class="o">-</span><span class="n">ads1x15</span> <span class="n">pandas</span>
+</pre></div>
+</div>
+<p>check that requirements are met using</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="nb">list</span>
+</pre></div>
+</div>
+<p>you should run you code within the virtual environment
+to leave the virtual environment simply type:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">deactivate</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="running-thonny-on-rapberry-pi">
+<h2>Running thonny on Rapberry Pi<a class="headerlink" href="#running-thonny-on-rapberry-pi" title="Permalink to this headline">¶</a></h2>
 </div>
 <div class="section" id="construction-of-the-measurement-board-and-connection-to-the-raspberry">
 <h2>Construction of the measurement board and connection to the Raspberry<a class="headerlink" href="#construction-of-the-measurement-board-and-connection-to-the-raspberry" title="Permalink to this headline">¶</a></h2>

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